ccsmeth

ccsmeth copied to clipboard

IndexError while running ccsmeth call_mods

10

I'm getting the following error and after this the job seems to be idling. it does not exit out and give me an error but instead keeps running without producing...

suvi93

Hi PengNi I'm trying to test ccsmeth with HG002 and I'm noticing a big difference in the number of results produced using count method as model, is this normal? The...

HITzhongyu

Extract features file

2

Dear, I align the ccs.bam to genome using ccsmeth align and the output is input into ccsmeth extract as follows. But I get empty file and without any error stdout....

yycunc

Index error during align_reads in denovo mode

2

Hi there, I'm getting the below error after the call_mods has generated the bam file and I use it to align to ref. It generated the `pbmm2.bam` file but could...

Surbhigrewal

Extract features file structure

15

Hi, I used ccsmeth extract command to extract features. How should it be structured when opened in tsv file in python? Could you please give some information related to the...

RahelehSalehi

calling modifications on Pacbio Revio platform

1

Dear authors, thanks for your great tool 'ccsmeth'. I try calling modifications on a hifi.bam generated from Pacbio Revio platform. However, I only get a empty bam files. I have...

eric-hy

Hi, I wanted to train ccsmeth on  my data, I changed batch_size several times, but still I have this error after some internal epochs. Could you...

RahelehSalehi

Normalization

1

Hi Peng, Thanks again for sharing your code. I was wondering did you normalize the data in training? I realized you normalized the data when you extracted the features.

RahelehSalehi

CCSMETH TRAIN

3

Hello @PengNi I want clarity on using the **ccsmeth train** to train a new model, please what is the component in the --train_file TRAIN_FILE because this was not well described...

olaraym

All reads are skipped/failed

4

Hi PengNi! I recently installed the ccsmeth and encountered a problem when using 'call_mods'. The command I used is `CUDA_VISIBLE_DEVICES=0 ccsmeth call_mods --input test.hifi_reads.aligned.bam --ref reference.fasta --model_file model_ccsmeth_5mCpG_call_mods_attbigru2s_b21.v2.ckpt --output test.hifi_reads.aligned.call_mods...

dnalinkbi